2VSC Cell Adhesion date Apr 22, 2008
title Structure Of The Immunoglobulin-Superfamily Ectodomain Of Human Cd47
authors D.Hatherley, S.C.Graham, J.Turner, K.Harlos, D.I.Stuart, A.N.Barclay
compound source
Molecule: Leukocyte Surface Antigen Cd47
Chain: A, B, C, D
Fragment: Immunoglobulin-Superfamily Ectodomain, Residues 19-136;
Synonym: Integrin-Associated Protein, Iap, Antigenic Surface Determinant Protein Oa3, Protein Mer6, Cd47;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Cricetulus Griseus
Expression_system_taxid: 10029
Expression_system_variant: Lec3.2.8.1
Expression_system_cell_line: Cho Cells
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pee14
symmetry Space Group: C 1 2 1
R_factor 0.216 R_Free 0.263
crystal
cell
length a length b length c angle alpha angle beta angle gamma
201.137 47.502 56.811 90.00 99.31 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand MG, NAG, PCA enzyme
Primary referencePaired receptor specificity explained by structures of signal regulatory proteins alone and complexed with CD47., Hatherley D, Graham SC, Turner J, Harlos K, Stuart DI, Barclay AN, Mol Cell. 2008 Jul 25;31(2):266-77. PMID:18657508
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (178 Kb) [Save to disk]
  • Biological Unit Coordinates (2vsc.pdb1.gz) 86 Kb
  • Biological Unit Coordinates (2vsc.pdb2.gz) 85 Kb
  • LPC: Ligand-Protein Contacts for 2VSC
  • CSU: Contacts of Structural Units for 2VSC
  • Likely Quarternary Molecular Structure file(s) for 2VSC
  • Structure Factors (566 Kb)
  • Retrieve 2VSC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VSC from S2C, [Save to disk]
  • Re-refined 2vsc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VSC in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2VSC
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2VSC, from MSDmotif at EBI
  • Fold representative 2vsc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vsc_B] [2vsc_D] [2vsc] [2vsc_C] [2vsc_A]
  • SWISS-PROT database: [Q08722]
  • Domain organization of [CD47_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 2VSC with the sequences similar proteins can be viewed for 2VSC's classification [CD47_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [CD47_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2VSC
  • Community annotation for 2VSC at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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